Next Generation Sequencing Bioinformatics

Next generation sequencing has become an essential tool in genetic and
genomic analysis. It is increasingly important for experimental
scientists to gain the bioinformatics skills required to assess and
analyse the large volumes of sequencing data produced by next generation
sequencers. This next generation sequencing bioinformatics course aims to
equip participants with the essential informatics skills and knowledge
required to begin analysing next generation sequencing data and carry out
some of the most common types of analysis.

The course programme will cover the algorithmic theory and principles of
bioinformatics, with a strong focus on practical computational sessions
using sequence analysis techniques and tools applicable to any species or
genome size. Accompanying the lecture and practical sessions will be a
series of seminars by invited speakers, who will highlight their
ground-breaking work in applications of next generation sequencing.

Learning Outcomes
On completion of the course, participants can expect to have acquired:

• A working knowledge of the unix command-line and writing basic shell scripts for automating bioinformatics tasks
• Knowledge of how to do QC assessment of high throughput sequencing data
• Understanding of the algorithmic concepts behind short read alignment and variant calling, and practical experience using the software
• Experience analysing RNA-Seq and CHiP-seq data for measuring abundance
• Knowledge of the organisation and sequencing data types available in public sequencing repositories

Please note: The practical sessions will be taught
exclusively through Unix/Linux. Therefore, participants are required to
have some previous exposure of using the Linux operating system. This
will be essential for participants to fully benefit from the course. The
course aims to provide a hands-on introduction to bioinformatics for next
generation sequencing, and should not be considered a complete education
in the theoretical and mathematical foundations of the topics. This
course is aimed at applicants solely interested in analysis of NGS data.
Applicants interested in practical, laboratory-based training in NGS
technologies and methodologies should consider our Next Generation
Sequencing lab course. Details of the 2017 lab course can be found
here and is next scheduled for April 2018.
Email us
for updates.

Feedback from the 2016 Next Generation Sequencing Bioinformatics
course

• Excellent course, highly recommended to anyone interested in bioinformatics whether they have some knowledge or want to start analysing their own data. Wonderful instructors and selection of participants and instructors. Very thankful that the opportunity was given to me.
• I enjoied the course very much. I am going to use many of the techniques that I have learned in my research.
• I would like to thank everyone involved in organization of the course! Well done! And I wish you keep it at the same great level and spread knowledge in this friendly atmosphere.
• Thank you so much for the wonderful week, it opened a new world for me.
• Thank you so much for everything! It was a life changing experience for me!

The hands-on programme will cover several aspects of next generation
sequencing data analysis, including lectures, discussions and practical
computational sessions covering the following:

• Introduction to NGS technologies and tour of Sanger Institute facilities
• Introduction to the unix command line
• Introduction to scripting for bioinformatics
• NGS data formats and tools
• Sequence alignment+QC
• SNP/indel theory and practical
• Structural variation theory and practical
• RNA-seq analysis
• ChiP-seq analysis
• Sequencing data visualisation with the Integrated Genomics Viewer
• Accessing public sequencing repositories
• Participant projects and presentations (final day)

Learning Outcomes
On completion of the course, participants can expect to have acquired:

• A working knowledge of the unix command-line and writing basic shell scripts for automating bioinformatics tasks
• Knowledge of how to do QC assessment of high throughput sequencing data
• Understanding
  of the algorithmic concepts behind short read alignment and variant
  calling, and practical experience using the software
• Experience analysing RNA-Seq and CHiP-seq data for measuring abundance
• Knowledge of the organisation and sequencing data types available in public sequencing repositories

Course lead instructors
Thomas
Keane EMBL-European Bioinformatics Institute, UK
Jacqui
Keane Wellcome Trust Sanger Institute, UK

Guest speakers
Kate Baker University of Liverpool, UK
Gosia Trynka Wellcome Trust Sanger
Institute, UK
Steven Munger The Jackson Laboratory, USA
Alejandro Sanchez-Flores National
Autonomous University of Mexico

Prerequisites
Applicants should be postdoctoral scientists, senior PhD students, junior
faculty members or clinicians/healthcare professionals actively engaged
in or soon to commence research involving next generation sequencing data
analysis.

Linux experience: The practical sessions will be taught exclusively
through Unix/Linux. Therefore, participants are required to have some
previous exposure of using the Linux operating system. This will be
essential for participants to fully benefit from the course.

Cost
The
course is subsidised by the Wellcome Genome Campus
Advanced Courses and Scientific Conferences Programme. This is a
residential
course and there is a fee of £680 towards
board and lodging for non-commercial applicants. Please contact us for
the commercial fee.

Additional limited bursaries are available (up to 50%
of the course fee)
and are awarded on merit. Please see the “Bursaries”
tab for details.

Applications
Applications for this course can be completed online. If you have any
problems with the online application process, please contact us.

Please note: Applications
must be supported by a
recommendation from a scientific or clinical sponsor (e.g. supervisor or
head of department). A request for a supporting
statement will be sent
to your nominated sponsor automatically during
the application process.
Applicants must ensure that their sponsor
provides this supporting
statement by the application deadline. Applications without a supporting
statement cannot be considered.

Deadlines
Deadline for Applications: Closed

Travel visas
Please contact the
event organiser if you require a letter to support a travel visa
application. Note that letters will be provided to confirmed attendees.

Non-European Economic Area or Swiss nationals may be required to have a
visa to enter the UK.
Early application is strongly advised, as this process can take 6-8 weeks
or longer.

Please visit the following websites for further information:
UK Border Agency website and information for general visitors and business
visitors.

Cost
The
course is subsidised by the Wellcome Genome Campus Advanced Courses
and
Scientific Conferences Programme. This is a residential
course and
there is a fee of £680 towards board and lodging for
non-commercial applicants. Please contact us for the commercial fee.

Bursaries
Advanced Courses are subsidised for non-commercial applicants from
anywhere in the world. Additional, limited bursaries are
available (up
to 50% of the course fee) and are awarded on merit. If you would like to
apply for a
bursary, please complete the bursary section of the online
application
form.

Please note that both the applicant
and sponsor are required to provide
a justification for the
bursary as part of the application.

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK
courses.

Overseas Courses (held outside of the UK)
A
limited number of bursaries are available for each course. These are
awarded on merit to cover travel, accommodation and sustenance. The
maximum award for travel (economy class) will be £750.

Bursaries can be applied for as part of the course application form.
Applicants
will be notified of a bursary award along with their place on
the
course, usually within one month of the application deadline. The
decision of the selection committee is
final.